# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1364830097 18000
# Node ID b61f1466ce8f1f32ce9d89d2ccbb7b9fb1ea033e
# Parent  217aedbdd0d0b7c14102baf943be5880fe2b8a22
Add tool_dependencies.xml and test case

diff -r 217aedbdd0d0 -r b61f1466ce8f README
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Mon Apr 01 10:28:17 2013 -0500
@@ -0,0 +1,19 @@
+
+== ea-utils Galaxy Wrapper ==
+
+This is a Galaxy wrapper for some ea-utils tools, fastq-join and sam-stats.
+
+** Installation **
+
+Installation from a tool shed provides the necessary tool dependencies.
+
+Otherwise, make sure fastq-join and sam-stats are in the path.
+Move the test data files to your galaxy root test-data.
+Move the xml files to a subdirectory of your tools directory and add lines in tool_conf.xml to point to them.
+Restart the Galaxy server.
+
+** Attribution **
+
+The ea-utils package and associated documentation can be found at: http://code.google.com/p/ea-utils/
+
+
diff -r 217aedbdd0d0 -r b61f1466ce8f fastq-mcf.xml
--- a/fastq-mcf.xml	Tue Mar 13 14:44:46 2012 -0400
+++ b/fastq-mcf.xml	Mon Apr 01 10:28:17 2013 -0500
@@ -1,7 +1,7 @@
 <tool id="fastq_mcf" name="FastqMcf" version="1.0">
   <description>sequence quality filtering and clipping</description>
   <requirements>
-    <requirement type="binary">fastq-mcf</requirement>
+    <requirement type="package" version="1.1.2-484">ea-utils</requirement>
   </requirements>
   <version_string>fastq-mcf -V</version_string>
   <command>fastq-mcf 
@@ -41,7 +41,9 @@
       #if len($trimming.sampcnt.__str__) > 0
         -s $trimming.sampcnt
       #end if
-      $trimming.ilv3
+      #if len($trimming.ilv3.__str__.strip()) > 0
+        -$trimming.ilv3
+      #end if
       $trimming.rmns
     #end if
     #if $noclip == True :
@@ -120,9 +122,9 @@
         </param>
         <param name="rmns" type="boolean" truevalue="-R" falsevalue="" checked="false" label="-R Don't remove N's from the fronts/ends of reads"/>
         <param name="ilv3" type="select" label="illumina PF filtering">
-           <option value=" ">Default</option>
-           <option value="-U">Disable illumina PF filtering</option>
-           <option value="-u">Enable illumina PF filtering</option>
+           <option value="">Default</option>
+           <option value="U">Disable illumina PF filtering</option>
+           <option value="u">Enable illumina PF filtering</option>
         </param>
       </when>
     </conditional>
@@ -143,7 +145,24 @@
       <filter>(noclip == False and mates != None)</filter>
     </data>
   </outputs>
+  <stdio>
+    <exit_code range="1:"  level="fatal"   description="Error" />
+  </stdio>
   <tests>
+    <test>
+      <param name="adpaters" ftype="fasta" value="adapters.fa" />
+      <param name="reads" ftype="fastqillumina" value="test_mcf_reads.fq" />
+      <param name="mates" ftype="fastqillumina" value="test_mcf_mates.fq" />
+      <param name="choice" value="user_set" />
+      <param name="nkeep" value="16" />
+      <param name="qthr" value="15" />
+      <param name="qwin" value="5" />
+      <param name="pctns" value="10" />
+      <param name="ilv3" value="u" />
+      <param name="phred" value="33" />
+      <output name="reads_out" file="testout_mcf_reads.fq" />
+      <output name="mates_out" file="testout_mcf_mates.fq" />
+    </test>
   </tests>
   <help>
 **What it does**
@@ -156,6 +175,8 @@
   Detect N's, and remove from ends
   Remove reads with CASAVA 'Y' flag (purity filtering)
   Discard sequences that are too short after all of the above
+
+
   Keep multiple mate-reads in sync while doing all of the above
 
 .. _fastq-mcf: http://code.google.com/p/ea-utils/wiki/FastqMcf
diff -r 217aedbdd0d0 -r b61f1466ce8f test-data/adapters.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/adapters.fa	Mon Apr 01 10:28:17 2013 -0500
@@ -0,0 +1,2 @@
+>Trufseq_Universal_Adaptor
+AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
diff -r 217aedbdd0d0 -r b61f1466ce8f test-data/test_mcf_mates.fq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_mcf_mates.fq	Mon Apr 01 10:28:17 2013 -0500
@@ -0,0 +1,20 @@
+@3VFXHS1:278:D13Y4ACXX:1:1101:1472:2209 2:N:0:CGATGT
+CTGGATTTGAAATCTTTAGCGGAGCGGGAACGCCGGCGCGGAAGGGTCTCTACACAGGGCCCGGTCCGCCCTTGCGCTCTCCTTAATGNNNNNNNNNNCGC
++
+@CCF?EFFHHHGHHHIFGI@HGGIEHIGIJGI6@@E>B8>??:DBD++399>ACCDDDD@DBDD58@BBDDDDD@@<@BDDDDC>CDC#############
+@3VFXHS1:278:D13Y4ACXX:1:1101:1434:2224 2:N:0:CGATGT
+CCCGGGGCCTCCCATTAAGGTCGCACTTGGACCCATTGCCATAGGTCTGGCTGTGGTAGCGTTTAAGACGATGCTGCTTGGAGGCCTTGGCTGTTTCATCA
++
+BCCFFFFDHFFHGIHIHGJJIJJGGIIJJJIDHGJIJEIIIIIJJIIJIJHHHEEF;>DDA>BBB@CAABBBDDCDDDDDDAD@@?CDDDCCB?ACCDDC#
+@3VFXHS1:278:D13Y4ACXX:1:1101:1712:2247 2:N:0:CGATGT
+GTTACTCAGCATTTATTCATGCCTGCTGTGTACGGAAAGGGCAGTTACAAAGGAAAGCCTTGATGATTCTGCTTCCAAGAAACGTGAAGATCAGATAATAT
++
+CBCFFFFFHHHHHJIJJIIJJJJJIIJIHIHIJJJIJIJIJJIIIIIIJJGGIIJJJIJJJJHIJJJJHIJHGHHHHFFFFFEDECBDDDDDCCDDDCDEE
+@3VFXHS1:278:D13Y4ACXX:1:1101:3318:2215 2:N:0:CGATGT
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAACAGAAAAAGAAAGAAGGAAAGGNGAGT
++
+CCCFFFFFHHHHHJJJJFHHHJJJIJJGGIDGHIEIJJJIIJGIJ5@FHIB?DFFEEEDEEEDD?####################################
+@3VFXHS1:278:D13Y4ACXX:2:1101:5344:2243 2:N:0:ACAGTG
+GGATCGGGAAAGGGGGGGGGGGGGGAAAAGGGGGGATTTCCGGGGGGGCCGGTTCTTTTAAAAAAAAAAAAAAAGAAAACAGAAACAGAAGATGGACAACA
++
+CCCFFFFFHHHHHJJJJFHHHJJJIJJGGIDGHIEIJJJIIJGIJ5@FHIB?DFFEEEDEEEDD?####################################
diff -r 217aedbdd0d0 -r b61f1466ce8f test-data/test_mcf_reads.fq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_mcf_reads.fq	Mon Apr 01 10:28:17 2013 -0500
@@ -0,0 +1,20 @@
+@3VFXHS1:278:D13Y4ACXX:1:1101:1472:2209 1:N:0:CGATGT
+CTGGTATTGTCTCTTCCCACACTGAACTCTGGGGAATTCGATGTGTGGCACAGCCCGGCTCAGCCTGCCCGCTGGTGGGAGCCCCTGGGAAGCTGCGGCGC
++
+@@CFDDFFGH>CAEH:CGHIJJJJEIHJJHIJJJ?DHIDIJHGEGHJG;FHC9@B(5@6A=EH:B@B@2=>>B?BDCBD<B52<<ABD?<?B1@A9>B###
+@3VFXHS1:278:D13Y4ACXX:1:1101:1434:2224 1:N:0:CGATGT
+GGCAGAGCCAATCTTCGGACGTGGTGATTGTCTCCTCTAAGTACAAACAGCGCTATGAGTGTCGCCTGCCAGCTGGAGCTATTCACTTCCAGCGTGAAAGG
++
+BC@FFFFFHHHGFHIIJJIJGFHICFCGIHGFHFGGCHD@F?B?BGGHJJIG6D@EHEHHEHCD259?AACD@AC59?,(5>A,;>:@C(::(029?8>@A
+@3VFXHS1:278:D13Y4ACXX:1:1101:1712:2247 1:N:0:CGATGT
+GTACACTTGAACACATTTTTCTAACCTTAGAAAATACCTACAAGGCCTGTTGTCTTGACCCATTACTCAATTGTCCCTGGCATATTATCTGATCTTCACGT
++
+CCCFFFFFHHHHGJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIJGIIJGGGDHHHIHIHHEIJIJJIIGGIIIIFEHHHHFEFFFDEEEDCEEEDEDC?A
+@3VFXHS1:278:D13Y4ACXX:1:1101:3318:2215 1:N:0:CGATGT
+AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAGAAAAAAAAACAAGCGACAAGGACAGA
++
+CCCFFFFFHHHHHJJJJJIJJJJJJJJJIJGHFFHIAHIFGGIIJJIJJFIJIHJIHHHGEGFE>CFFEB###############################
+@3VFXHS1:278:D13Y4ACXX:2:1101:5344:2243 1:N:0:ACAGTG
+GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAACAACAGAAAAAACAAAGCGCGAACAGTGC
++
+CCCFFFFFHHHHHJIJJIJIJHJJJJJJJHIGIGIHJFHFFDIIJGIIIJJJHHFIJJJJJJHCEHHFD################################
diff -r 217aedbdd0d0 -r b61f1466ce8f test-data/testout_mcf_mates.fq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/testout_mcf_mates.fq	Mon Apr 01 10:28:17 2013 -0500
@@ -0,0 +1,20 @@
+@3VFXHS1:278:D13Y4ACXX:1:1101:1472:2209 2:N:0:CGATGT
+CTGGATTTGAAATCTTTAGCGGAGCGGGAACGCCGGCGCGGAAGGGTCTCTACACAGGGCCCGGTCCGCCCTTGCGCTCTCCTTAATG
++
+@CCF?EFFHHHGHHHIFGI@HGGIEHIGIJGI6@@E>B8>??:DBD++399>ACCDDDD@DBDD58@BBDDDDD@@<@BDDDDC>CDC
+@3VFXHS1:278:D13Y4ACXX:1:1101:1434:2224 2:N:0:CGATGT
+CCCGGGGCCTCCCATTAAGGTCGCACTTGGACCCATTGCCATAGGTCTGGCTGTGGTAGCGTTTAAGACGATGCTGCTTGGAGGCCTTGGCTGTTTCATC
++
+BCCFFFFDHFFHGIHIHGJJIJJGGIIJJJIDHGJIJEIIIIIJJIIJIJHHHEEF;>DDA>BBB@CAABBBDDCDDDDDDAD@@?CDDDCCB?ACCDDC
+@3VFXHS1:278:D13Y4ACXX:1:1101:1712:2247 2:N:0:CGATGT
+GTTACTCAGCATTTATTCATGCCTGCTGTGTACGGAAAGGGCAGTTACAAAGGAAAGCCTTGATGATTCTGCTTCCAAGAAACGTGAAGATCAGATAATAT
++
+CBCFFFFFHHHHHJIJJIIJJJJJIIJIHIHIJJJIJIJIJJIIIIIIJJGGIIJJJIJJJJHIJJJJHIJHGHHHHFFFFFEDECBDDDDDCCDDDCDEE
+@3VFXHS1:278:D13Y4ACXX:1:1101:3318:2215 2:N:0:CGATGT
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAA
++
+CCCFFFFFHHHHHJJJJFHHHJJJIJJGGIDGHIEIJJJIIJGIJ5@FHIB?DFFEEEDEEEDD?
+@3VFXHS1:278:D13Y4ACXX:2:1101:5344:2243 2:N:0:ACAGTG
+GGATCGGGAAAGGGGGGGGGGGGGGAAAAGGGGGGATTTCCGGGGGGGCCGGTTCTTTTAAAAAA
++
+CCCFFFFFHHHHHJJJJFHHHJJJIJJGGIDGHIEIJJJIIJGIJ5@FHIB?DFFEEEDEEEDD?
diff -r 217aedbdd0d0 -r b61f1466ce8f test-data/testout_mcf_reads.fq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/testout_mcf_reads.fq	Mon Apr 01 10:28:17 2013 -0500
@@ -0,0 +1,20 @@
+@3VFXHS1:278:D13Y4ACXX:1:1101:1472:2209 1:N:0:CGATGT
+CTGGTATTGTCTCTTCCCACACTGAACTCTGGGGAATTCGATGTGTGGCACAGCCCGGCTCAGCCTGCCCGCTGGTGGGAGCCCCTGGGAAGCTGCGG
++
+@@CFDDFFGH>CAEH:CGHIJJJJEIHJJHIJJJ?DHIDIJHGEGHJG;FHC9@B(5@6A=EH:B@B@2=>>B?BDCBD<B52<<ABD?<?B1@A9>B
+@3VFXHS1:278:D13Y4ACXX:1:1101:1434:2224 1:N:0:CGATGT
+GGCAGAGCCAATCTTCGGACGTGGTGATTGTCTCCTCTAAGTACAAACAGCGCTATGAGTGTCGCCTGCCAGCTGGAGCTATTCACTTCCAGCGTGAAAGG
++
+BC@FFFFFHHHGFHIIJJIJGFHICFCGIHGFHFGGCHD@F?B?BGGHJJIG6D@EHEHHEHCD259?AACD@AC59?,(5>A,;>:@C(::(029?8>@A
+@3VFXHS1:278:D13Y4ACXX:1:1101:1712:2247 1:N:0:CGATGT
+GTACACTTGAACACATTTTTCTAACCTTAGAAAATACCTACAAGGCCTGTTGTCTTGACCCATTACTCAATTGTCCCTGGCATATTATCTGATCTTCACGT
++
+CCCFFFFFHHHHGJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIJGIIJGGGDHHHIHIHHEIJIJJIIGGIIIIFEHHHHFEFFFDEEEDCEEEDEDC?A
+@3VFXHS1:278:D13Y4ACXX:1:1101:3318:2215 1:N:0:CGATGT
+AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTGAAAAAA
++
+CCCFFFFFHHHHHJJJJJIJJJJJJJJJIJGHFFHIAHIFGGIIJJIJJFIJIHJIHHHGEGFE>CFFEB
+@3VFXHS1:278:D13Y4ACXX:2:1101:5344:2243 1:N:0:ACAGTG
+GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTGAAAAAA
++
+CCCFFFFFHHHHHJIJJIJIJHJJJJJJJHIGIGIHJFHFFDIIJGIIIJJJHHFIJJJJJJHCEHHFD
diff -r 217aedbdd0d0 -r b61f1466ce8f tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Apr 01 10:28:17 2013 -0500
@@ -0,0 +1,23 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="ea-utils" version="1.1.2-484">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://ea-utils.googlecode.com/files/ea-utils.1.1.2-484.tar.gz</action>
+                <!-- Unable to get varcall to compile properly we don't need it, so skip -->
+                <action type="shell_command">sed -i.bak 's/varcall$//' Makefile</action>
+                <action type="shell_command">PREFIX=$INSTALL_DIR make install</action>
+                <!-- For some reason, this is not installed by the Makefile, so move it ourselves -->
+                <action type="move_file">
+                    <source>sam-stats</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+        </readme>
+    </package>
+</tool_dependency>